- PDB-3luu: Crystal structure of Protein with unknown function which belongs ... -
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基本情報
登録情報
データベース: PDB / ID: 3luu
タイトル
Crystal structure of Protein with unknown function which belongs to Pfam DUF971 family (AFE_2189) from Acidithiobacillus ferrooxidans ATCC 23270 at 1.93 A resolution
要素
Uncharacterized protein
キーワード
BIOSYNTHETIC PROTEIN / AFE_2189 / Pfam DUF971 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / quinone biosynthesis
THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
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実験情報
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実験
実験
手法: X線回折 / 使用した結晶の数: 1
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試料調製
結晶
マシュー密度: 2.43 Å3/Da / 溶媒含有率: 49.33 %
結晶化
温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.3 詳細: 0.3000M magnesium chloride, 22.0000% polyethylene glycol 8000, 0.1M TRIS pH 8.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
解像度: 1.93→41.471 Å / Num. obs: 8966 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / 冗長度: 7.09 % / Biso Wilson estimate: 24.109 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 11.86
反射 シェル
解像度 (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.93-2
1.211
1.97
6364
873
1
99.7
2-2.08
1.211
2.5
6294
866
1
97.1
2.08-2.17
1.211
3.2
6020
838
1
99.3
2.17-2.29
1.211
4.1
6654
916
1
98.6
2.29-2.43
1.211
5.9
6169
851
1
98.3
2.43-2.62
1.211
7.1
6461
900
1
98.6
2.62-2.88
1.211
10.9
6348
892
1
99
2.88-3.3
1.211
15.6
6465
919
1
98.7
3.3-4.15
1.211
26.6
6348
914
1
99.1
4.15-41.471
1.211
36.1
6470
1007
1
98.6
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位相決定
位相決定
手法: 多波長異常分散
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解析
ソフトウェア
名称
バージョン
分類
NB
REFMAC
5.5.0102
精密化
PHENIX
精密化
SHELX
位相決定
MolProbity
3beta29
モデル構築
XSCALE
データスケーリング
PDB_EXTRACT
3.006
データ抽出
XDS
データ削減
SHELXD
位相決定
autoSHARP
位相決定
精密化
構造決定の手法: 多波長異常分散 / 解像度: 1.93→41.471 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 7.106 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.131 立体化学のターゲット値: MAXIMUM LIKELIHOOD WITH PHASES 詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...詳細: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. THE METAL ZINC WAS ASSIGNED AS ZINC (ZN) BASED ON X-RAY FLURORESCENCE SPECTROSCOPY AND ANOMALOUS DIFFERENCE FOURIERS. 5. CHLORIDE (CL) MODELED WAS PRESENT IN CRYSTALLIZATION CONDITION.
Rfactor
反射数
%反射
Selection details
Rfree
0.221
427
4.8 %
RANDOM
Rwork
0.196
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obs
0.197
8946
98.85 %
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溶媒の処理
イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK